SMED30028271

Overview
NameSMED30028271
Smed IDSMED30028271
Length (bp)2303
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)



Explore this single cell expression dataset with our NB Cluster Shiny App



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30028271 (SMED30028271) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30028271 (SMED30028271) in cells (dots) of each of the 12 neoblast clusters.

 

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Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
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Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020



SMED30028271

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30028271h1SMcG0019645 SmedASXL_007119SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30028271h1SMcG0019645 SmedASXL_007119SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30028271h1SMcG0019645 dd_Smed_v6_10452_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30028271h1SMcG0019645 OX_Smed_1.0.03067ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30028271 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006353:4749..8832 +11389
Homology
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BLAST of SMED30028271 vs. Planmine SMEST
Match: SMESG000014735.1 (SMESG000014735.1)

HSP 1 Score: 1264.6 bits (3271), Expect = 0.000e+0
Identity = 666/666 (100.00%), Postives = 666/666 (100.00%), Query Frame = 1 
Query:  178 MHDFSMKLPKDVYKDCRQSGECYIFVNKKVPRYEAVQTCKDYNGSVVLINDPAENEWIAARLKSLKFSHSYLNAKYDKNLQIYLTSEGSMAGFVNSQPPFELLFESKSKNNHRRTKRHARVHKSSLRRVVVYKHIGKRRIVYVKYKSSKRINKVKHIYRFKYRKFLQKYENKFKQKLKLYKIIVAQKTRKIREEKLKLFQIWISRIEWLKKQNWENWFESIKEIDKTLWXXXXXXXXXXXXXXXXXXVDFKWNAWWTKILNWYRDWIKQFSKKQIDMIWKWKQFLVWLKKNSWEKSITYISGIDQELWKARIKRIIWVIEERKYVDICDKDWSGWKTTVEAWIKMANEKRKDILDNDKKRLTIEKWKKRLDWIQQHHIDLLIKFGNASSDWKNKALAVLENVKNYIKNYDIDSLSGANLLSQWQEIKKQTEKDLTEFYLPKDVQTILGWINGFHWLESNNIQYILQHQGGPKEKTEYERFESIIKGNKYSPENFREISEIFPRLKSLIENQXXXXXXXXXXXXXXXXXXXVVNYFNIPINNSLHPLDLPRSIDALKDLAKNYPSLEIFLINHLTKLHYLARKFSENKFEPHQILFEKLIRDHVAILERLKLPLNFWKLLSTMDFPSLSINLKRGDCLTMENNGRTPELWQQISCNRPQQFICQIKS 2175
            MHDFSMKLPKDVYKDCRQSGECYIFVNKKVPRYEAVQTCKDYNGSVVLINDPAENEWIAARLKSLKFSHSYLNAKYDKNLQIYLTSEGSMAGFVNSQPPFELLFESKSKNNHRRTKRHARVHKSSLRRVVVYKHIGKRRIVYVKYKSSKRINKVKHIYRFKYRKFLQKYENKFKQKLKLYKIIVAQKTRKIREEKLKLFQIWISRIEWLKKQNWENWFESIKEIDKTLWINRIREIIDIINKKSIDSVDFKWNAWWTKILNWYRDWIKQFSKKQIDMIWKWKQFLVWLKKNSWEKSITYISGIDQELWKARIKRIIWVIEERKYVDICDKDWSGWKTTVEAWIKMANEKRKDILDNDKKRLTIEKWKKRLDWIQQHHIDLLIKFGNASSDWKNKALAVLENVKNYIKNYDIDSLSGANLLSQWQEIKKQTEKDLTEFYLPKDVQTILGWINGFHWLESNNIQYILQHQGGPKEKTEYERFESIIKGNKYSPENFREISEIFPRLKSLIENQKSSAIKGISDISIIRKSRSVVNYFNIPINNSLHPLDLPRSIDALKDLAKNYPSLEIFLINHLTKLHYLARKFSENKFEPHQILFEKLIRDHVAILERLKLPLNFWKLLSTMDFPSLSINLKRGDCLTMENNGRTPELWQQISCNRPQQFICQIKS
Sbjct:    1 MHDFSMKLPKDVYKDCRQSGECYIFVNKKVPRYEAVQTCKDYNGSVVLINDPAENEWIAARLKSLKFSHSYLNAKYDKNLQIYLTSEGSMAGFVNSQPPFELLFESKSKNNHRRTKRHARVHKSSLRRVVVYKHIGKRRIVYVKYKSSKRINKVKHIYRFKYRKFLQKYENKFKQKLKLYKIIVAQKTRKIREEKLKLFQIWISRIEWLKKQNWENWFESIKEIDKTLWINRIREIIDIINKKSIDSVDFKWNAWWTKILNWYRDWIKQFSKKQIDMIWKWKQFLVWLKKNSWEKSITYISGIDQELWKARIKRIIWVIEERKYVDICDKDWSGWKTTVEAWIKMANEKRKDILDNDKKRLTIEKWKKRLDWIQQHHIDLLIKFGNASSDWKNKALAVLENVKNYIKNYDIDSLSGANLLSQWQEIKKQTEKDLTEFYLPKDVQTILGWINGFHWLESNNIQYILQHQGGPKEKTEYERFESIIKGNKYSPENFREISEIFPRLKSLIENQKSSAIKGISDISIIRKSRSVVNYFNIPINNSLHPLDLPRSIDALKDLAKNYPSLEIFLINHLTKLHYLARKFSENKFEPHQILFEKLIRDHVAILERLKLPLNFWKLLSTMDFPSLSINLKRGDCLTMENNGRTPELWQQISCNRPQQFICQIKS 666
[Close]
BLAST of SMED30028271 vs. Planmine SMEST
Match: SMESG000014735.1 (SMESG000014735.1)

HSP 1 Score: 1252.27 bits (3239), Expect = 0.000e+0
Identity = 661/661 (100.00%), Postives = 661/661 (100.00%), Query Frame = 1 
Query:  193 MKLPKDVYKDCRQSGECYIFVNKKVPRYEAVQTCKDYNGSVVLINDPAENEWIAARLKSLKFSHSYLNAKYDKNLQIYLTSEGSMAGFVNSQPPFELLFESKSKNNHRRTKRHARVHKSSLRRVVVYKHIGKRRIVYVKYKSSKRINKVKHIYRFKYRKFLQKYENKFKQKLKLYKIIVAQKTRKIREEKLKLFQIWISRIEWLKKQNWENWFESIKEIDKTLWXXXXXXXXXXXXXXXXXXVDFKWNAWWTKILNWYRDWIKQFSKKQIDMIWKWKQFLVWLKKNSWEKSITYISGIDQELWKARIKRIIWVIEERKYVDICDKDWSGWKTTVEAWIKMANEKRKDILDNDKKRLTIEKWKKRLDWIQQHHIDLLIKFGNASSDWKNKALAVLENVKNYIKNYDIDSLSGANLLSQWQEIKKQTEKDLTEFYLPKDVQTILGWINGFHWLESNNIQYILQHQGGPKEKTEYERFESIIKGNKYSPENFREISEIFPRLKSLIENQXXXXXXXXXXXXXXXXXXXVVNYFNIPINNSLHPLDLPRSIDALKDLAKNYPSLEIFLINHLTKLHYLARKFSENKFEPHQILFEKLIRDHVAILERLKLPLNFWKLLSTMDFPSLSINLKRGDCLTMENNGRTPELWQQISCNRPQQFICQIKS 2175
            MKLPKDVYKDCRQSGECYIFVNKKVPRYEAVQTCKDYNGSVVLINDPAENEWIAARLKSLKFSHSYLNAKYDKNLQIYLTSEGSMAGFVNSQPPFELLFESKSKNNHRRTKRHARVHKSSLRRVVVYKHIGKRRIVYVKYKSSKRINKVKHIYRFKYRKFLQKYENKFKQKLKLYKIIVAQKTRKIREEKLKLFQIWISRIEWLKKQNWENWFESIKEIDKTLWINRIREIIDIINKKSIDSVDFKWNAWWTKILNWYRDWIKQFSKKQIDMIWKWKQFLVWLKKNSWEKSITYISGIDQELWKARIKRIIWVIEERKYVDICDKDWSGWKTTVEAWIKMANEKRKDILDNDKKRLTIEKWKKRLDWIQQHHIDLLIKFGNASSDWKNKALAVLENVKNYIKNYDIDSLSGANLLSQWQEIKKQTEKDLTEFYLPKDVQTILGWINGFHWLESNNIQYILQHQGGPKEKTEYERFESIIKGNKYSPENFREISEIFPRLKSLIENQKSSAIKGISDISIIRKSRSVVNYFNIPINNSLHPLDLPRSIDALKDLAKNYPSLEIFLINHLTKLHYLARKFSENKFEPHQILFEKLIRDHVAILERLKLPLNFWKLLSTMDFPSLSINLKRGDCLTMENNGRTPELWQQISCNRPQQFICQIKS
Sbjct:    1 MKLPKDVYKDCRQSGECYIFVNKKVPRYEAVQTCKDYNGSVVLINDPAENEWIAARLKSLKFSHSYLNAKYDKNLQIYLTSEGSMAGFVNSQPPFELLFESKSKNNHRRTKRHARVHKSSLRRVVVYKHIGKRRIVYVKYKSSKRINKVKHIYRFKYRKFLQKYENKFKQKLKLYKIIVAQKTRKIREEKLKLFQIWISRIEWLKKQNWENWFESIKEIDKTLWINRIREIIDIINKKSIDSVDFKWNAWWTKILNWYRDWIKQFSKKQIDMIWKWKQFLVWLKKNSWEKSITYISGIDQELWKARIKRIIWVIEERKYVDICDKDWSGWKTTVEAWIKMANEKRKDILDNDKKRLTIEKWKKRLDWIQQHHIDLLIKFGNASSDWKNKALAVLENVKNYIKNYDIDSLSGANLLSQWQEIKKQTEKDLTEFYLPKDVQTILGWINGFHWLESNNIQYILQHQGGPKEKTEYERFESIIKGNKYSPENFREISEIFPRLKSLIENQKSSAIKGISDISIIRKSRSVVNYFNIPINNSLHPLDLPRSIDALKDLAKNYPSLEIFLINHLTKLHYLARKFSENKFEPHQILFEKLIRDHVAILERLKLPLNFWKLLSTMDFPSLSINLKRGDCLTMENNGRTPELWQQISCNRPQQFICQIKS 661
The following BLAST results are available for this feature:
BLAST of SMED30028271 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30028271 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30028271 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30028271 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30028271 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30028271 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30028271 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30028271 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30028271 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30028271 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30028271 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30028271 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30028271 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30028271 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000014735.10.000e+0100.00SMESG000014735.1[more]
SMESG000014735.10.000e+0100.00SMESG000014735.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028271 ID=SMED30028271|Name=SMED30028271|organism=Schmidtea mediterranea sexual|type=transcript|length=2303bp
AACATTTGGTAGAAAATCTGTTTATGTTGACTTTTGTTGTAAACAAAGAA
ATGTGTCGACTTGTTTTCTGTTCCTAGATTTATAAAAGATTTGACCAGTC
CGATTTTATATATTTTTCTAATGTTTCTTGTGATAATTTCTTTACTTTTA
CCCTTGCTCAATGGACAACAGCTAAGGATGCACGATTTCTCCATGAAGCT
TCCAAAAGATGTTTACAAAGATTGTCGACAATCGGGGGAGTGTTATATAT
TTGTAAATAAAAAGGTGCCTCGGTATGAGGCAGTTCAAACTTGCAAAGAT
TATAATGGATCTGTGGTCTTGATAAATGACCCAGCTGAAAATGAATGGAT
AGCCGCAAGGCTCAAGTCTTTGAAGTTTTCTCATTCATATTTGAATGCAA
AATATGACAAAAATTTACAAATTTACCTCACATCCGAAGGGTCAATGGCA
GGCTTTGTTAACTCTCAACCTCCATTTGAACTATTATTCGAGAGTAAATC
CAAAAATAATCATCGGAGAACCAAGCGTCACGCAAGGGTTCACAAATCGA
GCCTTCGGCGAGTGGTAGTCTATAAACACATTGGCAAACGGCGAATCGTC
TACGTCAAATACAAATCCTCGAAACGTATCAACAAAGTCAAGCATATCTA
TCGTTTTAAGTACCGGAAATTTCTGCAAAAATATGAAAACAAATTCAAAC
AAAAATTGAAATTGTACAAAATAATTGTTGCTCAAAAAACTCGAAAAATT
CGAGAAGAAAAATTGAAATTATTTCAAATTTGGATTTCAAGAATCGAATG
GTTAAAAAAACAAAATTGGGAAAATTGGTTTGAATCGATCAAAGAAATCG
ATAAAACACTTTGGATCAATCGGATCAGAGAAATAATCGACATAATCAAC
AAGAAATCGATTGATTCGGTAGATTTCAAATGGAATGCCTGGTGGACAAA
AATCCTCAACTGGTATCGAGATTGGATCAAACAGTTTTCGAAAAAACAAA
TCGACATGATCTGGAAATGGAAGCAATTCCTAGTTTGGTTGAAAAAGAAT
TCGTGGGAAAAATCTATTACATACATTTCCGGAATTGATCAGGAACTATG
GAAAGCCAGAATCAAGAGAATTATTTGGGTGATTGAAGAGAGAAAATACG
TTGACATTTGCGACAAAGATTGGTCGGGATGGAAAACGACAGTTGAGGCG
TGGATTAAAATGGCCAACGAAAAACGAAAAGACATTTTGGATAATGACAA
AAAACGATTGACTATCGAAAAATGGAAAAAACGACTCGACTGGATCCAAC
AACATCATATTGATCTATTGATAAAGTTCGGAAACGCTTCTTCCGATTGG
AAAAATAAAGCATTGGCTGTTTTAGAAAATGTTAAAAACTATATTAAAAA
TTATGACATTGATTCGCTATCGGGTGCGAATCTTCTCAGCCAATGGCAGG
AGATCAAAAAACAAACGGAAAAAGATCTCACTGAGTTTTATCTACCAAAA
GATGTTCAAACAATTCTCGGATGGATAAACGGTTTCCATTGGTTGGAAAG
CAACAATATCCAATACATCCTTCAGCATCAGGGGGGACCCAAAGAAAAAA
CCGAATACGAGCGGTTTGAATCCATAATCAAAGGAAACAAATATTCCCCA
GAAAATTTCCGAGAGATATCGGAAATATTCCCCCGACTAAAAAGTTTAAT
AGAAAACCAGAAAAGTTCTGCCATTAAAGGCATCAGTGACATTTCTATAA
TAAGGAAATCGAGATCTGTTGTAAATTATTTTAATATCCCAATCAATAAT
TCACTTCATCCACTTGATCTTCCTCGATCAATTGATGCGTTGAAAGATTT
GGCAAAAAATTATCCTTCTCTGGAAATTTTCCTAATTAATCATCTGACGA
AACTTCATTATCTGGCAAGGAAATTTTCTGAAAATAAGTTTGAACCTCAT
CAAATTCTATTTGAAAAACTGATCCGGGATCACGTGGCTATCCTCGAGCG
ATTGAAGTTGCCATTGAATTTCTGGAAATTACTGTCTACAATGGACTTCC
CAAGTTTATCTATCAATCTAAAGCGAGGCGATTGCCTAACAATGGAAAAC
AATGGGCGAACTCCGGAATTGTGGCAGCAGATTAGTTGCAACAGACCTCA
ACAATTCATTTGCCAAATCAAATCATGAGGGGCTCTGCAATTTTAAACAA
GAGAAAATAACTGATATAATTTTCCATATAATTTTGTTGGTTATATTAAA
GAGATATTTCAGTCAAAGCCGATTGAGCTTTTGCTTTGTGTTTCTAGTCA
AAG
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protein sequence of SMED30028271-orf-1

>SMED30028271-orf-1 ID=SMED30028271-orf-1|Name=SMED30028271-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=686bp
MFLVIISLLLPLLNGQQLRMHDFSMKLPKDVYKDCRQSGECYIFVNKKVP
RYEAVQTCKDYNGSVVLINDPAENEWIAARLKSLKFSHSYLNAKYDKNLQ
IYLTSEGSMAGFVNSQPPFELLFESKSKNNHRRTKRHARVHKSSLRRVVV
YKHIGKRRIVYVKYKSSKRINKVKHIYRFKYRKFLQKYENKFKQKLKLYK
IIVAQKTRKIREEKLKLFQIWISRIEWLKKQNWENWFESIKEIDKTLWIN
RIREIIDIINKKSIDSVDFKWNAWWTKILNWYRDWIKQFSKKQIDMIWKW
KQFLVWLKKNSWEKSITYISGIDQELWKARIKRIIWVIEERKYVDICDKD
WSGWKTTVEAWIKMANEKRKDILDNDKKRLTIEKWKKRLDWIQQHHIDLL
IKFGNASSDWKNKALAVLENVKNYIKNYDIDSLSGANLLSQWQEIKKQTE
KDLTEFYLPKDVQTILGWINGFHWLESNNIQYILQHQGGPKEKTEYERFE
SIIKGNKYSPENFREISEIFPRLKSLIENQKSSAIKGISDISIIRKSRSV
VNYFNIPINNSLHPLDLPRSIDALKDLAKNYPSLEIFLINHLTKLHYLAR
KFSENKFEPHQILFEKLIRDHVAILERLKLPLNFWKLLSTMDFPSLSINL
KRGDCLTMENNGRTPELWQQISCNRPQQFICQIKS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0000420parapharyngeal region
Vocabulary: INTERPRO
TermDefinition
IPR016186C-type_lectin-like/link_sf
IPR016187CTDL_fold
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR016186C-type lectin-like/link domain superfamilyGENE3DG3DSA:3.10.100.10coord: 20..146
e-value: 4.1E-8
score: 34.9
NoneNo IPR availableCDDcd00037CLECTcoord: 41..108
e-value: 3.53463E-7
score: 47.2294
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..15
score: 0.816
IPR016187C-type lectin foldSUPERFAMILYSSF56436C-type lectin-likecoord: 38..117